file_tag = sprintf("%s_%s", cell_type_name, graph_weight)
assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag),
what = character(), sep="\n")
gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 32.00 36.75 38.00 37.58 39.00 42.00
## [1] 40
## [1] 32 33 34 34 35 35 36 36 36 36 37 37 37 37 37 37 37 37 37 38 38 38 38 38 38
## [26] 38 38 38 39 39 39 40 40 40 40 40 40 41 41 42
bioMart.All the gene symbols that can be found in bioMart are
consistent with what we have. So no need to run it.
ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")
gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"),
filters = "external_gene_name",
values = assayed_genes,
mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]
table(assayed_genes %in% gene_BM$external_gene_name)
t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]
table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]alias2Symbol function from
limma.a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
gi = assayed_genes[i]
ai = alias2Symbol(gi)
if(length(ai) > 1){
print(gi)
print(ai)
}
a2s[i] = ai[1]
}
table(is.na(a2s))##
## FALSE TRUE
## 1739 261
##
## FALSE TRUE <NA>
## 21 1718 261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)
gene_info[sym_in_data != sym_limma,]## sym_in_data sym_limma
## 1: LRRC6 DNAAF11
## 2: C11orf49 CSTPP1
## 3: LINC00476 ERCC6L2-AS1
## 4: HNRNPA1P48 HNRNPA1L3
## 5: ZRANB2-AS2 ZRANB2-DT
## 6: LINC00271 AHI1-DT
## 7: RFX3-AS1 RFX3-DT
## 8: LINC00884 ATP13A3-DT
## 9: FBXO30-DT EPM2A-DT
## 10: LINC00894 EOLA2-DT
## 11: COX10-AS1 COX10-DT
## 12: LINC01184 SLC12A2-DT
## 13: FAM198B-AS1 GASK1B-AS1
## 14: C5orf17 LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16: LINC01146 HISLA
## 17: BTBD11 ABTB3
## 18: H2BU1 H2BC26
## 19: SKIV2L SKIC2
## 20: FAM155A NALF1
## 21: CTB-41I6.2 PIK3R5-DT
## sym_in_data sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")),
gene_symbol := sym_limma]
dim(gene_info)## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## 3: PDK4 PDK4 PDK4
## 4: CALCR CALCR CALCR
## 5: ABCB4 ABCB4 ABCB4
## t1
## 1
## 2000
Gene set annotations (by gene symbols) were downloaded from MSigDB website.
gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]] = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"
pathways = list()
for(k1 in names(gmtfile)){
pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}
names(pathways)## [1] "reactome" "go_bp"
## reactome go_bp
## 1692 7647
Filter gene sets for size between 10 and 500.
## $reactome
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 7.0 9.0 12.0 17.0 23.0 31.0 44.0 71.8 120.9 1463.0
##
## $go_bp
## 0% 10% 20% 30% 40% 50% 60% 70% 80% 90% 100%
## 5.0 6.0 8.0 10.0 14.0 19.0 29.0 46.0 80.8 183.0 1966.0
## [1] 2000 3
## sym_in_data sym_limma gene_symbol
## 1: CFTR CFTR CFTR
## 2: ICA1 ICA1 ICA1
## [1] 36517 9
## gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003 FALSE TSPAN6 NCBITaxon:9606
## 2: ENSG00000000005 FALSE TNMD NCBITaxon:9606
## feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1: gene 76 0.002350 99.8100
## 2: gene 1 0.000025 99.9975
## total_counts
## 1: 94
## 2: 1
## [1] 2000
##
## TRUE
## 2000
##
## FALSE TRUE
## 34517 2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1
table(gene_dat$selected)##
## 0 1
## 34517 2000
## $`0`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.00 94.48 99.58 93.53 99.97 100.00
##
## $`1`
## Min. 1st Qu. Median Mean 3rd Qu. Max.
## 0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data",
by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)## [1] 2000 12
## sym_in_data sym_limma gene_symbol gene_ids feature_is_filtered
## 1: AATK AATK AATK ENSG00000181409 FALSE
## 2: ABAT ABAT ABAT ENSG00000183044 FALSE
## feature_reference feature_biotype n_cells_by_counts mean_counts
## 1: NCBITaxon:9606 gene 3157 0.091525
## 2: NCBITaxon:9606 gene 9074 0.368950
## pct_dropout_by_counts total_counts selected
## 1: 92.1075 3661 1
## 2: 77.3150 14758 1
max_n2kp = 10
goseq_res = NULL
for(k in 1:length(gene_sets)){
if(length(gene_sets[[k]]) < 10) { next }
print(k)
set_k = paste0("set_", k)
print(gene_sets[[k]])
genes = gene_info$sym_in_data %in% gene_sets[[k]]
names(genes) = gene_info$gene_symbol
table(genes)
pwf = nullp(genes, "hg38", "geneSymbol",
bias.data = 100 - gene_info$pct_dropout_by_counts)
for(k1 in names(pathways)){
p1 = pathways[[k1]]
res1 = goseq(pwf, "hg38", "geneSymbol",
gene2cat=goseq:::reversemapping(p1))
res1$FDR = p.adjust(res1$over_represented_pvalue, method="BH")
nD = sum(res1$FDR < 0.05)
if(nD > 0){
res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
res1$category = gsub("_", " ", res1$category)
res1$category = tolower(res1$category)
res1$category = substr(res1$category, start=1, stop=81)
goseq_res[[set_k]][[k1]] = res1
}
}
}## [1] 1
## [1] "SYT7" "CDH20" "NALCN" "ARFGEF3"
## [5] "ADAM23" "DNAH6" "CHD5" "CSMD2"
## [9] "PCSK2" "ATP8A2" "CBLN2" "STXBP5L"
## [13] "TENM2" "CNTN5" "ZNF385D" "AK5"
## [17] "CLSTN2" "ANKRD30BL" "RANBP3L" "ADGRV1"
## [21] "AMER2" "GREM1" "FSTL5" "FUT9"
## [25] "HPSE2" "SRRM3" "SSTR2" "FLRT2"
## [29] "CACNA1E" "LINC00632" "BASP1-AS1" "ROR1-AS1"
## [33] "RP11-191L9.4" "AC093843.1" "LINC01435" "RP11-384F7.2"
## [37] "CTC-340A15.2" "SLC5A4-AS1" "CTC-535M15.2" "RMST"
## [41] "RP11-436D23.1"
## [1] 2
## [1] "PDK4" "ABCB4" "CPED1" "GASK1A"
## [5] "SESN3" "TENM4" "GASK1B" "FOLR2"
## [9] "ARHGAP42" "PLD4" "CYSLTR1" "C5orf64"
## [13] "RAB39A" "CLEC9A" "MAMDC2-AS1" "AC003090.1"
## [17] "LMCD1-AS1" "HDAC2-AS2" "LINC02642" "RP11-634B7.4"
## [21] "COX10-AS1" "AC008697.1" "LINC01301" "LINC01094"
## [25] "MAILR" "MIR3142HG" "RP11-946L16.1" "RP11-554D14.6"
## [29] "RP11-187O7.3" "MRC1" "MIR222HG" "MIR223HG"
## [33] "LINC00506" "RP11-323F24.5" "RP11-685G11.1" "RP11-4F5.3"
## [37] "CPM" "KCNE1"
## [1] 3
## [1] "SIGLEC1" "ADGRD1" "F13A1" "LILRB2"
## [5] "ENOSF1" "IFI44L" "CH25H" "FHAD1"
## [9] "TMEM163" "ADAMTS15" "PGBD5" "ODF3B"
## [13] "PLCXD3" "MS4A4E" "RP11-445F6.2" "LINC01515"
## [17] "AC092431.3" "LINC02008" "BDNF-AS" "LINC02211"
## [21] "LINC02432" "C5orf17" "LINC02196" "FAM66D"
## [25] "OVCH1-AS1" "RP11-72M17.1" "CTD-2336H13.2" "LINC02073"
## [29] "RP11-154H12.3" "RP11-354K4.2" "CCDC28A-AS1" "LINC01374"
## [33] "RP11-281A20.2" "CERNA2" "RP11-221G19.1" "RP11-321P16.3"
## [37] "RP13-52K8.2"
## [1] 4
## [1] "ACER3" "CARMIL1" "SYNDIG1" "FAM149A"
## [5] "TBC1D14" "NPL" "NKD1" "AOPEP"
## [9] "DISP1" "SAMSN1" "DEPTOR" "DENND2B"
## [13] "ATF7IP2" "TMC7" "SPTLC3" "SCAI"
## [17] "ZDHHC14" "KCNQ3" "PRKN" "RANBP17"
## [21] "LINC02649" "MIR99AHG" "RP1-30E17.2" "HMGA1P4"
## [25] "ZFPM2-AS1" "RP11-10H3.1" "RP11-692P14.1" "RP6-91H8.6"
## [29] "ARHGAP6" "KCNQ2" "RAP1GAP" "PILRA"
## [33] "GRK3" "PADI2" "SEC14L1" "SLC2A13"
## [37] "KCNQ5" "LNCAROD"
## [1] 5
## [1] "MGLL" "PRTFDC1" "NIPAL2" "MAP2K6"
## [5] "IFT43" "CCDC18" "SSPN" "GSTCD"
## [9] "MED12L" "FILIP1L" "GPR34" "CENPP"
## [13] "RP5-1132H15.1" "RMDN2-AS1" "RP11-692D12.1" "LINC00624"
## [17] "HGF" "TGFB2" "TMED8" "CLNK"
## [21] "HPCAL1" "TOX2" "TMEM115" "GYPC"
## [25] "FAM117B" "CCDC40" "IQGAP2" "HTR7"
## [29] "PARP8" "PCNT" "RHOBTB3" "ABCA1"
## [33] "GLRX" "GOLIM4" "EFCAB2" "SLC48A1"
## [37] "SBF2-AS1" "RP11-154H23.4"
## [1] 6
## [1] "HHAT" "ZNF821" "MOBP" "AATK" "ST3GAL1"
## [6] "FAM50A" "RGS1" "MTMR8" "ADAP1" "MEGF9"
## [11] "SNX25" "DARS1" "CDH26" "SEM1" "AFDN"
## [16] "KIAA0513" "GPNMB" "CCNG2" "ARHGAP18" "TIAM2"
## [21] "RSU1" "FRRS1" "ABCG1" "ANKZF1" "MARCHF8"
## [26] "APLF" "MFSD4B" "ZC3H6" "DPYD" "PARVB"
## [31] "H1-0" "CYRIA" "GCC2-AS1" "AC093818.1" "PIK3IP1-DT"
## [36] "MIR181A1HG" "IFITM10" "CLEC5A"
## [1] 7
## [1] "SLC4A7" "EPB41L2" "POLA1" "TGFBR1" "SIPA1L2" "BIN1"
## [7] "BACH1" "SOCS6" "SH3RF3" "FNDC3B" "TRIP11" "TJP1"
## [13] "ARHGEF10" "DDX5" "GAB1" "E2F3" "P4HA1" "RASSF8"
## [19] "RUNX2" "ARHGAP22" "UACA" "FNBP1L" "MSN" "MCPH1"
## [25] "MGAT5" "RUNX1" "ZNF143" "AXL" "LDLRAD4" "ALCAM"
## [31] "PEAK1" "SND1"
## [1] 8
## [1] "PDE10A" "GNLY" "ADAMTS19" "GLT1D1"
## [5] "BANK1" "ADAMTS3" "UCN" "MT1E"
## [9] "TMEM151B" "RFLNA" "ZNF804B" "LINC01277"
## [13] "AC073115.7" "AC002539.1" "RP3-525N10.2" "LINC00271"
## [17] "KIF5C-AS1" "LINC02884" "AC007682.1" "AC073115.6"
## [21] "MIR4300HG" "STARD4-AS1" "LINC00923" "LINC02055"
## [25] "RP4-809F18.1" "MTRNR2L8" "LINC02316" "PSMD7-DT"
## [29] "RP11-621L6.2" "RP11-58G13.1" "RP11-413N10.3" "RP11-640F22.1"
## [33] "LINC02885" "RP11-38B6.1" "RP11-320L2.1" "RP11-341N18.1"
## [1] 9
## [1] "HTR2B" "PNMA3" "ZNRF1" "NFIX" "NSMAF" "PDE8A"
## [7] "GRAMD4" "FOSL2" "TBC1D2" "PCSK5" "RNF24" "BNIP3L"
## [13] "GYS1" "PPARD" "PFKFB4" "GBE1" "PAPOLG" "NR4A3"
## [19] "ATF1" "KDM6B" "PHF21A" "GLUL" "GABARAPL1" "PELI2"
## [25] "GNA12" "SLC25A37" "ARID5B" "CFDP1" "MAPK13" "SPRY1"
## [31] "NFIL3" "PPIP5K1" "KLHL6" "PPP1R3B" "BNIP3" "TRNAU1AP"
## [37] "LIMK2"
## [1] 10
## [1] "SCMH1" "KIFAP3"
## [3] "APBB1IP" "TMEM156"
## [5] "SPATA6" "FRMD6"
## [7] "KCNMB1" "RASGEF1C"
## [9] "KCNMA1" "AUTS2"
## [11] "TAGAP" "TMEM52B"
## [13] "NAV2" "ZNF608"
## [15] "TLN2" "GAP43"
## [17] "OLR1" "DLEU1"
## [19] "B3GNT5" "NCKAP5"
## [21] "SPATA13_ENSG00000182957" "SLC8A1"
## [23] "SFMBT2" "MBD5"
## [25] "TMSB4X" "LTC4S"
## [27] "RP11-557H15.4" "LINC02232"
## [29] "RP11-419I17.1" "RNASET2"
## [31] "RGCC" "ZBTB46"
## [33] "PCGF5" "FMN1"
## [1] 11
## [1] "MUSK" "EFR3B"
## [3] "PROCR" "CRYM"
## [5] "STMN2" "ECM2"
## [7] "OPRM1" "PODXL2"
## [9] "NEK11" "WLS"
## [11] "IFIT3" "IFIT2"
## [13] "FMO5" "ABCA8"
## [15] "MMS22L" "IER2"
## [17] "FAM227B" "BEAN1"
## [19] "GLYATL1" "MYO5B"
## [21] "SLC35G2" "CPLX1"
## [23] "DTWD2" "DENND5B"
## [25] "GRIK1" "PC"
## [27] "MCMDC2" "TSPYL2"
## [29] "IFIT1" "STMN3"
## [31] "H2BC18" "SMCR5"
## [33] "GPRC5D-AS1" "LINC01605_ENSG00000253161"
## [35] "RP11-867G2.8" "RP11-314L11.1"
## [37] "TMEM140"
## [1] 12
## [1] "PLPP1" "HAMP" "AZIN2" "SHOC1"
## [5] "NLGN4Y" "MICOS10" "ADGRG2" "TTTY14"
## [9] "FLJ40194" "DLEU7" "COL25A1" "EDNRB-AS1"
## [13] "ENTPD1-AS1" "SLC8A1-AS1" "RP11-202G18.1" "HCG22"
## [17] "CCDC26" "RP11-142M10.2" "LINC00884" "RNASEH2B-AS1"
## [21] "RP11-353M9.1" "CCDC200" "RP11-360F5.1" "LINC02057"
## [25] "LINC01258" "RP11-238K6.1" "RP11-624C23.1" "RP11-452H21.1"
## [29] "SMIM35" "RP11-196H14.2" "RP11-136F16.1" "LINC00621"
## [33] "CEACAM16-AS1" "RP11-399K21.11" "LINC02712" "RP11-323P17.2"
## [37] "RP11-264E23.4" "RP11-13J12.3"
## [1] 13
## [1] "ATP8B1" "SLC5A9" "SGCE" "PDE5A"
## [5] "ENO4" "FAM177B" "INSYN2B" "ANKUB1"
## [9] "AC002463.3" "ARHGAP26-AS1" "AC017101.10" "AC096558.1"
## [13] "SRGAP2-AS1" "AC083884.8" "AC037445.1" "RP11-666F17.1"
## [17] "CPB2-AS1" "MYCBP2-AS1" "DIAPH2-AS1" "AC018890.6"
## [21] "CTD-2015H6.3" "CTD-2227I18.1" "RHOQ-AS1" "RP11-649G15.2"
## [25] "AP000487.6" "RP11-513G19.1" "USP3-AS1" "RP11-815J21.4"
## [29] "RP11-16B9.1" "ABHD15-AS1" "RP11-16C1.3" "RP11-793A3.2"
## [33] "RP11-53B2.3" "CTD-2282P23.2" "RP11-793H13.14" "DISC2"
## [37] "RP11-65F13.4" "RP11-1146N6.3" "AC009505.4"
## [1] 14
## [1] "ZFP64" "NEXMIF" "CASS4" "PITPNM2"
## [5] "PLCL1" "BEX1" "RALGPS1" "GPAT3"
## [9] "RAB40B" "NRGN" "TSPAN7" "PLXDC1"
## [13] "SMIM14" "NXN" "MIR31HG" "MACROD2"
## [17] "FIGN" "LIPE-AS1" "ALOX12-AS1" "KIF9-AS1"
## [21] "RP11-120D5.1" "RP11-246A10.1" "MRPS30-DT" "RP11-370I10.6"
## [25] "LINC01572" "RP11-495L19.1" "TENM1" "ADGRL1"
## [29] "GDF11" "PLXNC1" "CFAP161" "ST3GAL2"
## [33] "CXXC5" "CDH4" "ANKS1B" "CTD-3088G3.8"
## [37] "SYCP2" "RORB" "LL22NC03-2H8.5"
## [1] 15
## [1] "ADAM28" "ST6GAL1" "IPCEF1" "PLAT" "IGSF21"
## [6] "RCAN3" "PLAU" "ITPR2" "ABCC4" "C3"
## [11] "FOXP2" "LYVE1" "GARNL3" "GIPC2" "GAREM1"
## [16] "AIG1" "FRMD4A" "PRMT9" "CX3CR1" "P2RY12"
## [21] "LRRC8C" "CA8" "SLC9A9" "CH17-55D9.1" "ARHGAP15"
## [26] "SLC1A3" "IL27RA" "LIFR" "FOXP1" "OGFRL1"
## [31] "SLC41A2" "CSGALNACT1" "JAZF1" "MTSS1" "BNC2"
## [36] "MAML2" "IFNLR1"
## [1] 16
## [1] "HIVEP2" "SLC9A7" "HDHD5" "MAP3K20"
## [5] "ARRDC2" "AK1" "STN1" "MXI1"
## [9] "GTDC1" "ATP8A1" "CEMIP2" "RASGEF1B"
## [13] "PGGHG" "ST18" "SLC26A7" "ZFYVE28"
## [17] "KLF13" "RESF1" "LPCAT4" "RBM44"
## [21] "TMTC2" "TNFAIP8L3" "NCMAP" "ZNF395"
## [25] "TPRG1" "ERO1A" "LINC02397" "AS3MT"
## [29] "FAM229A" "SGO1-AS1" "DIRC3" "DARS1-AS1"
## [33] "LINC01762" "AF064858.8" "RP11-305L7.3" "FMNL1-DT"
## [37] "LINC01138" "MYOCOS" "RP11-344F5.1" "RP11-249L21.6"
## [1] 17
## [1] "MMP24" "GLIPR1L1" "EYS" "FSIP2"
## [5] "SPDYE2" "HDAC4-AS1" "ELMO1-AS1" "TMLHE-AS1"
## [9] "HNRNPA1P48" "LINC01375" "AC105461.1" "RP11-165F24.3"
## [13] "RP11-526K17.2" "ALG13-AS1" "RP1-225E12.2" "COA6-AS1"
## [17] "RP11-528G1.2" "RP11-575L7.8" "BCL2L1-AS1" "DENND6A-AS1"
## [21] "ZBTB20-AS5" "LINC00960" "RP11-712B9.2" "MEF2C-AS2"
## [25] "RP11-268P4.5" "RP11-39E3.3" "RP11-506H20.1" "RP11-434H14.1"
## [29] "RP11-370I10.2" "CTD-2647E9.3" "RP11-317G6.1" "RP11-703M24.5"
## [33] "CTD-3149D2.4" "RP4-769N13.7" "RP1-256G22.2" "RP11-121C2.3"
## [37] "RP11-7F3.1" "RP11-685G9.5" "RP11-555K12.4" "RP11-56I23.2"
## [1] 18
## [1] "ZFY" "SLC26A3"
## [3] "PCDH11Y" "PXDNL"
## [5] "NR6A1" "SEMA3E"
## [7] "FUT10" "LRRC3B"
## [9] "CCDC73" "POTEG"
## [11] "RP11-37N22.1" "AC023469.1"
## [13] "AC067959.1" "RP11-147G16.1"
## [15] "RP11-154D17.1" "MYO16-AS1"
## [17] "AC013463.2" "LINC02646"
## [19] "AC002066.1" "CTD-2643I7.5"
## [21] "RP11-696N14.1" "RP11-17A1.3"
## [23] "RP11-259O2.1" "RP11-79E3.2"
## [25] "LINC01609" "RP11-351A11.1"
## [27] "RP11-13N12.1" "RP11-20D14.3"
## [29] "MTRNR2L12" "RMRP_ENSG00000269900"
## [31] "SCARNA2_ENSG00000270066" "AGBL1"
## [33] "CH507-513H4.1" "CH507-528H12.1"
## [35] "RP11-596C23.6" "RP4-799O8.1"
## [37] "RP11-322M13.1" "AC003099.2"
## [39] "RP11-398J12.1" "RP11-404C6.6"
## [1] 19
## [1] "RPL3" "RPL18A" "RPL19" "RPL34"
## [5] "RPL24" "FGF13" "MTHFS" "RPS24"
## [9] "PRDM5" "RPS2" "RPS11" "RPL11"
## [13] "SPAG16" "RPL32" "FAU" "ATG10"
## [17] "RPL26" "ELAVL4" "MRPL1" "RPL38"
## [21] "RPLP2" "RPS23" "SPATS2L" "CPNE4"
## [25] "RPL12" "RPL23A" "RPL39" "AIF1"
## [29] "RP11-535M15.1" "LINC01278" "PVT1" "RP11-37B2.1"
## [33] "SLC1A2" "LPL" "ADARB1" "LILRB3"
## [1] 20
## [1] "STS" "MID1" "CCDC170" "DOCK10" "IRF8"
## [6] "ITGA9" "AC097721.2" "XIST" "TWIST2" "MEI4"
## [11] "SCIN" "LCP2" "CTTNBP2" "DOCK9" "IRAK3"
## [16] "INTS6" "NCOA7" "TSHZ3" "PTPRE" "PRAM1"
## [21] "CCNH" "FAM13A" "SSH2" "USP53" "SDK1"
## [26] "DIXDC1" "FER" "ACSL1" "MERTK" "GPHN"
## [31] "CHD2" "CMSS1" "GPRIN3" "MITF" "RALGAPA2"
## [36] "PLCG2"
## [1] 21
## [1] "MPP2" "ATF5" "FGR" "LRRC7" "CDK14" "CDK17"
## [7] "ARHGAP10" "IGSF9B" "ITPKC" "HIVEP1" "FGF14" "POU6F2"
## [13] "CPE" "MOB3B" "RAMP1" "MACROD1" "PDZD2" "CNKSR2"
## [19] "ADGRL3" "LONRF1" "NCAM2" "SORCS3" "GMEB1" "CSMD3"
## [25] "CRADD" "NLGN1" "CTNND2" "PTGER4" "NEGR1" "CNTNAP2"
## [31] "CADM2" "ZBTB7A" "NRXN1" "ZBTB7C" "LSAMP" "NRG3"
## [37] "SNHG14"
## [1] 22
## [1] "ICA1" "MCF2L2" "IL1A" "ZRANB3" "EFCAB11"
## [6] "TCERG1L" "KCNMB2" "CTA-292E10.6" "LINC00996" "KCNQ1OT1"
## [11] "AC009166.9" "CNTN1" "NCDN" "HPCAL4" "SLC2A5"
## [16] "CACNA1B" "CACNA1C" "SCN3A" "CACNA2D1" "PTPRN2"
## [21] "SYN2" "SPTBN4" "EDIL3" "RBFOX3" "GRM5"
## [26] "KCND3" "DPP10" "MSRA" "PCDH9" "KCND2"
## [31] "PRKG1" "SYN3" "GRM7" "FAM153CP" "U91319.1"
## [1] 23
## [1] "CEACAM1" "SLC9B1" "RP11-281P23.2" "RP11-493L12.3"
## [5] "RP11-516C1.1" "CELSR3" "ABCA7" "PLEKHH3"
## [9] "ANO8" "MLF2" "GALNT16" "HELLS"
## [13] "TGFBI" "HIF3A" "CHI3L1" "FGF17"
## [17] "LYPD5" "TNFRSF11B" "ADCY5" "H2AC6"
## [21] "VMO1" "NHEJ1" "EME2" "ZNF521"
## [25] "ZDBF2" "AF064858.6" "SLC12A8" "RP11-384C4.7"
## [29] "RP3-467L1.4" "RP11-657O9.1" "ARHGEF25" "LINC01414"
## [33] "RP11-661A12.5" "MTRNR2L1" "RP11-429A20.3" "RP11-81K2.1"
## [37] "LINC00551"
## [1] 24
## [1] "ZDHHC19" "RP11-713N11.4" "PKD1" "SLC2A3"
## [5] "DDX3Y" "HACE1" "PPP1R15A" "GADD45B"
## [9] "RNMT" "FLT1" "IL4I1" "APBB3"
## [13] "USP9Y" "SPP1" "SRGN" "TREM1"
## [17] "MICAL2" "RGS16" "MYO10" "PLIN2"
## [21] "TAMALIN" "ALDH1A1" "DDIT4" "FAM210A"
## [25] "ADSS1" "ANKRD37" "IARS1" "H2BU1"
## [29] "CEBPD" "ZSCAN31" "HIF1A-AS3" "CTD-2285E13.1"
## [33] "RP11-134L10.2"
## [1] 25
## [1] "CALCR" "IL7" "NEURL2" "PIGC"
## [5] "ADGRA3" "ADGRG5" "RNF180" "LINC00476"
## [9] "IRAG1-AS1" "CATSPERE" "SDHAF3" "SCOC-AS1"
## [13] "PAPSS2" "CARNMT1-AS1" "ATP6AP1L" "ENTPD3-AS1"
## [17] "TMEM72-AS1" "TSBP1-AS1" "RP13-188A5.1" "RP5-1198O20.4"
## [21] "FSIP2-AS1" "IPO9-AS1" "UFL1-AS1" "RPL34-DT"
## [25] "RP11-195C7.1" "LRIG2-DT" "LINC01877" "RORA-AS1"
## [29] "STX18-AS1" "RP11-130F10.1" "LIX1-AS1" "DISC1FP1"
## [33] "RP11-160E2.6" "RP11-74J13.8" "EIF1B-AS1" "RP11-736I24.5"
## [37] "RP11-19D22.1" "RP11-622O11.6" "RP11-261A24.1" "RP11-237N2.1"
## [41] "RP1-236J16.3" "RP11-120L14.1"
## [1] 26
## [1] "ERCC8" "DHRS9" "ANGPT2" "CHN1"
## [5] "UBE2Q2" "BCL2A1" "TNFRSF21" "IRAK1BP1"
## [9] "TEX9" "ABCA5" "PAQR3" "LCLAT1"
## [13] "RP11-131L23.1" "RPL41" "VCAN" "KCNAB2"
## [17] "MYOM1" "KATNAL1" "SPOCK2" "SLC16A10"
## [21] "GABRG2" "CYTIP" "HIP1" "BTG1"
## [25] "PITPNC1" "RASA2" "ZMAT4" "OTUD1"
## [29] "ATOH8" "C11orf80" "MCTP1" "JAKMIP2"
## [33] "CD247" "TOX" "MIR155HG" "LUCAT1"
## [37] "RP11-475M20.2"
## [1] 27
## [1] "DERA" "TDRD3" "DAAM1" "GDAP1" "ARSB" "EPHB2"
## [7] "STAMBPL1" "NUBPL" "NFIA" "KIF26B" "ARHGAP25" "DYNC2H1"
## [13] "CCDC7" "CLEC16A" "LIMCH1" "RFX3" "PHLPP1" "RFX2"
## [19] "TRPS1" "PRKAG2" "SASH1" "ELL2" "IQSEC2" "IQSEC1"
## [25] "FARP1" "MSI2" "RBM47" "SLC43A2" "DHRSX" "AFF1"
## [31] "PACS1" "SAMD12" "SERTAD2" "GDI1"
## [1] 28
## [1] "RIPOR2" "DUOX1" "MCTP2" "TMEM44"
## [5] "LINC00467" "BEX3" "RAB37" "H2BC4"
## [9] "H2AC20" "MTCP1" "GOLGA8B" "AC023590.1"
## [13] "ZNF451-AS1" "WEE2-AS1" "PCDH9-AS2" "RP11-142A5.1"
## [17] "KCNMA1-AS1" "RP11-544A12.4" "RP5-1101C3.1" "RP11-115J16.1"
## [21] "RP11-120A1.1" "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"
## [25] "TCF4-AS1" "RP11-126O1.4" "TSIX" "H2AC19"
## [29] "RP11-386I14.4" "H2BC8" "H2AC8" "H2BC7"
## [33] "TRG-AS1" "RP11-275G7.2" "GS1-98E2.1" "RP11-21M24.6"
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"
## [1] 29
## [1] "CD74" "CST3" "OGN" "SLC2A9"
## [5] "FLVCR2" "XAF1" "ITM2C" "SMAD6"
## [9] "PTH2R" "LY96" "COPG2" "C1QC"
## [13] "S100Z" "C1QB" "RTTN" "PROS1"
## [17] "CHSY3" "FIRRE" "LINC00894" "RP11-574F11.4"
## [21] "TRHDE" "RASSF2" "MAN1A1" "FRMD4B"
## [25] "COL5A1" "CHSY1" "TLR2" "NGLY1"
## [29] "CDCP1" "NPTX1" "LRFN4" "TLR5"
## [33] "PELI1" "GK" "ZNF277" "UBXN2B"
## [37] "ZNF407"
## [1] 30
## [1] "PRDM11" "CFAP74" "RTN4RL1" "KCNT1"
## [5] "BICRAL" "SEMA6D" "ZNF365" "RBMS3"
## [9] "NPAS3" "SPOCK1" "CFAP251" "CAMK2N1"
## [13] "GABRB1" "LRFN5" "PDZRN4" "HTR1E"
## [17] "GPC5" "KCTD16" "GLDN" "PTPRT"
## [21] "NPIPB15" "ZNF846" "TAFA2" "FAM155A"
## [25] "MEG3" "MIAT" "RP5-864K19.4" "ARL17B"
## [29] "SHISA9" "RP11-111A21.1" "RP11-707P17.1" "RP11-368L12.1"
## [33] "RP11-396B14.2" "IQCJ-SCHIP1" "RP11-114N19.3" "RP11-358F13.1"
## [37] "RP11-335E8.3" "RP11-452F19.4"
## [1] 31
## [1] "TTC7A" "SP140" "ARHGEF18" "TMEM241"
## [5] "ARL5C" "BEND6" "ENPP3" "C4orf19"
## [9] "MAMDC2" "LIPC" "ZMAT3" "MARCHF3"
## [13] "SCFD2" "CDIN1" "KBTBD12" "LINC01356"
## [17] "LINC01357" "LINC00539" "AC105760.2" "LINC01141"
## [21] "LINC01684" "KCNMB2-AS1" "ARHGAP8" "XACT"
## [25] "PTCHD4" "LINC00968" "MEF2C-AS1" "RP11-541P9.3"
## [29] "ZNF10" "RP11-630C16.2" "RP11-493L12.4" "LINC00907"
## [33] "ATP6V0D1-DT" "RP11-437L7.2" "RP11-111G13.1" "RP4-545L17.11"
## [37] "RP11-168F24.3" "STAB1" "AC025171.1" "CTB-41I6.2"
## [1] 32
## [1] "ZNF532" "OPHN1" "PIGL" "MS4A4A" "TENT5A"
## [6] "LDAH" "MTERF1" "PUDP" "SLC49A4" "FBN2"
## [11] "WDPCP" "PID1" "CLIC2" "RAB28" "NMNAT3"
## [16] "TMEM144" "CCDC171" "ACYP2" "FGGY" "WDR25"
## [21] "PCED1B" "RNLS" "B3GLCT" "LINC01285" "PRDX6-AS1"
## [26] "ZNF433-AS1" "FTCDNL1" "SLC16A1-AS1" "TEX41" "ZRANB2-AS2"
## [31] "RFX3-AS1" "LINC01376" "LINC01184" "RP11-319G6.1" "CTB-161M19.4"
## [36] "C8orf37-AS1" "PRANCR" "LINC01146" "MMP28" "RP1-111C20.3"
## [1] 33
## [1] "OSBPL6" "PDE4D" "RALGPS2" "RFC3" "PIGK" "MAGI1"
## [7] "PTPN14" "SETBP1" "TIAM1" "PLEKHA7" "ATAD5" "DNAH14"
## [13] "WWC3" "PLEKHA5" "PDE4A" "CUX2" "RLF" "ESYT2"
## [19] "DENND1A" "MAPK8IP1" "STARD13" "AGAP3" "DENND4C" "WDR45B"
## [25] "RIT2" "SRSF12" "AGAP1" "FAM110B" "ROBO1" "TANC2"
## [31] "FAM20C" "CADM1" "PDE4B" "SIPA1L1" "RGL3"
## [1] 34
## [1] "TXNDC16" "PCSK1N"
## [3] "LRRC6" "CALY"
## [5] "LPAR6" "UNC80"
## [7] "GPR85" "SKA2"
## [9] "ERC2" "COL5A2"
## [11] "AC011288.2" "ALG1L9P_ENSG00000248671"
## [13] "CTD-2537O9.1" "CEROX1"
## [15] "RP11-305E17.8" "COPG2IT1"
## [17] "ADAM22" "RAPGEF4"
## [19] "ANKRD12" "RAPGEF1"
## [21] "PPFIA2" "CDH18"
## [23] "FMN2" "FMNL2"
## [25] "CLASP2" "OXR1"
## [27] "LRP1B" "DLGAP1"
## [29] "RIMS2" "CSMD1"
## [31] "OPCML" "RALYL"
## [33] "KCNIP4" "MYT1L"
## [35] "MAGI2" "COL27A1"
## [37] "NEAT1" "SAP30-DT"
## [1] 35
## [1] "PRKCQ" "MTHFD2L" "PRKCH" "ARAP2" "ZFAT"
## [6] "MYO9A" "SESN1" "ZNF586" "DOCK3" "DCUN1D4"
## [11] "WNT2B" "RGL1" "CAMKMT" "AMN1" "RASGRP3"
## [16] "AGPAT5" "ADK" "CDC42SE2" "EPB41" "STARD9"
## [21] "NEK10" "RNF150" "MALT1" "SLC35E3" "ZHX2"
## [26] "AIDA" "ARL4C" "CARD11" "LINC00862" "DENND1B"
## [31] "C17orf67" "SOGA3" "KLF3-AS1" "AC092835.2" "RP1-179N16.6"
## [36] "SELENOP" "HCG17" "C2orf27A"
## [1] 36
## [1] "MBNL3" "P3H2" "APBA1" "GCNT2"
## [5] "PEX7" "AKAP7" "SLC10A7" "RAB38"
## [9] "DTD1" "METTL25" "LANCL2" "DPH6"
## [13] "ARHGAP20" "ARMH4" "LRIG1" "CD226"
## [17] "MAP3K7CL" "TNFRSF13C" "PUS10" "MBOAT1"
## [21] "CAPS2" "LEKR1" "LIN52" "LINC00630"
## [25] "RP11-162D16.2" "MIR646HG" "C12orf75" "RP11-381K20.2"
## [29] "LINC02762" "GMDS-DT" "RP11-679C8.2" "LINC02328"
## [33] "RP11-323I15.5" "KLHL24" "SLC35E1" "IL15"
## [37] "TMEM65"
## [1] 37
## [1] "SLC26A4" "PLGRKT" "MAP3K8" "PLEK" "CENPK"
## [6] "MIS18BP1" "SAT1" "ZSCAN5A" "PCBD2" "EPSTI1"
## [11] "AHI1" "SLC22A23" "BCAS3" "TRPC1" "SLC25A25"
## [16] "C11orf49" "PSTPIP2" "CACNA1D" "BTG2" "ANO10"
## [21] "CDYL2" "PBX3" "XKR6" "MX2" "APOO"
## [26] "KIAA0825" "ZFP36L1" "SRGAP3" "CDKN2B-AS1" "JARID2"
## [31] "MSR1" "CTNNA2" "UBE2R2" "MGAT1" "RNF144B"
## [36] "TNFAIP8" "RASSF3" "ACOT11"
## [1] 38
## [1] "SNCAIP" "RPH3A" "LRRC74A" "MEIS1" "RORA" "RAB27A" "SMARCD3"
## [8] "CELF4" "TBL1X" "NPDC1" "EPHA4" "AKT3" "EMILIN2" "DRAM1"
## [15] "KCNH1" "PAM" "CLVS2" "LRRC4C" "CLEC1A" "CRIM1" "PDE3B"
## [22] "KALRN" "ZFPM2" "PPM1E" "ALOX15B" "ZDHHC20" "UNC5C" "TSHZ2"
## [29] "EFNA5" "NELL2" "OSBP2" "PBX1" "KAZN" "MIB2" "MICAL3"
## [36] "GRIN2B"
## [1] 39
## [1] "PKD2L2" "ANGPTL1" "CYREN" "ATP5F1E"
## [5] "OMD" "ACKR4" "IER3" "AGBL3"
## [9] "C11orf65" "CYTL1" "DNAJC24" "RP11-321C24.1"
## [13] "RP4-568F9.6" "ARHGAP15-AS1" "RAP2C-AS1" "LANCL1-AS1"
## [17] "ITGA9-AS1" "FBXO30-DT" "RP11-123B3.2" "RP1-117O3.2"
## [21] "KDM4A-AS1" "RP11-775D22.3" "RP11-796E2.4" "RP11-544A12.8"
## [25] "ANK2-AS1" "FAM198B-AS1" "AC006160.5" "CTD-3239E11.2"
## [29] "RP11-1H15.2" "RP11-571M6.7" "RP11-638I2.8" "RP11-66H6.3"
## [33] "PRKCA-AS1" "RP11-737O24.2" "RP11-622I12.1" "RP11-458A7.1"
## [37] "RP1-80B9.4" "RP11-1H15.4" "RP1-18C9.3" "RP11-6G22.1"
## [41] "CTD-2021K4.2"
## [1] 40
## [1] "ARSJ" "LINC00639" "RP11-617F9.2" "MAMLD1"
## [5] "RASGRP2" "COL5A3" "LILRB5" "HS3ST2"
## [9] "OLFM1" "PATJ" "BTBD11" "ME3"
## [13] "FBXO32" "PALM2AKAP2" "NRG2" "JAML"
## [17] "PLPP3" "SNED1" "PRICKLE2" "ARHGEF3"
## [21] "STXBP6" "TBC1D10C" "ADGRB1" "H1-10"
## [25] "SLIT1" "LINC00910" "CR1L" "LINC00970"
## [29] "XKR9" "LINC01320" "SATB1-AS1" "LIMD1-AS1"
## [33] "RP11-47I22.3" "CYP1B1-AS1" "TRHDE-AS1" "LINC01322"
## [37] "USP2-AS1" "CPEB2-DT" "RP5-1015P16.1" "RENO1"
for(n1 in names(goseq_res)){
k = as.numeric(gsub("set_", "", n1))
print(n1)
print(gene_sets[[k]])
print(goseq_res[[n1]])
}## [1] "set_15"
## [1] "ADAM28" "ST6GAL1" "IPCEF1" "PLAT" "IGSF21"
## [6] "RCAN3" "PLAU" "ITPR2" "ABCC4" "C3"
## [11] "FOXP2" "LYVE1" "GARNL3" "GIPC2" "GAREM1"
## [16] "AIG1" "FRMD4A" "PRMT9" "CX3CR1" "P2RY12"
## [21] "LRRC8C" "CA8" "SLC9A9" "CH17-55D9.1" "ARHGAP15"
## [26] "SLC1A3" "IL27RA" "LIFR" "FOXP1" "OGFRL1"
## [31] "SLC41A2" "CSGALNACT1" "JAZF1" "MTSS1" "BNC2"
## [36] "MAML2" "IFNLR1"
## $reactome
## category over_represented_pvalue under_represented_pvalue
## 241 dissolution of fibrin clot 3.91158e-05 1
## numDEInCat numInCat FDR
## 241 2 3 0.04623487
##
## [1] "set_19"
## [1] "RPL3" "RPL18A" "RPL19" "RPL34"
## [5] "RPL24" "FGF13" "MTHFS" "RPS24"
## [9] "PRDM5" "RPS2" "RPS11" "RPL11"
## [13] "SPAG16" "RPL32" "FAU" "ATG10"
## [17] "RPL26" "ELAVL4" "MRPL1" "RPL38"
## [21] "RPLP2" "RPS23" "SPATS2L" "CPNE4"
## [25] "RPL12" "RPL23A" "RPL39" "AIF1"
## [29] "RP11-535M15.1" "LINC01278" "PVT1" "RP11-37B2.1"
## [33] "SLC1A2" "LPL" "ADARB1" "LILRB3"
## $reactome
## category over_represented_pvalue
## 138 cellular response to starvation 0
## 301 eukaryotic translation elongation 0
## 302 eukaryotic translation initiation 0
## 452 influenza infection 0
## 557 metabolism of amino acids and derivatives 0
## 640 nonsense mediated decay nmd 0
## 801 regulation of expression of slits and robos 0
## 850 response of eif2ak4 gcn2 to amino acid deficiency 0
## 901 rrna processing 0
## 927 selenoamino acid metabolism 0
## under_represented_pvalue numDEInCat numInCat FDR
## 138 1 18 26 0
## 301 1 18 23 0
## 302 1 18 23 0
## 452 1 18 27 0
## 557 1 18 41 0
## 640 1 18 23 0
## 801 1 18 27 0
## 850 1 18 25 0
## 901 1 18 25 0
## 927 1 18 26 0
##
## $go_bp
## category over_represented_pvalue
## 630 cytoplasmic translation 0.000000e+00
## 4283 ribosome biogenesis 7.430974e-11
## 4279 ribosomal large subunit biogenesis 7.825622e-09
## 4278 ribosomal large subunit assembly 3.486725e-07
## 4281 ribosomal small subunit biogenesis 1.679751e-06
## 4282 ribosome assembly 1.700370e-06
## 3144 protein rna complex organization 6.151118e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 630 1.0000000 18 23 0.000000e+00
## 4283 1.0000000 8 13 1.753710e-07
## 4279 1.0000000 5 5 1.231231e-05
## 4278 1.0000000 4 4 4.114336e-04
## 4281 1.0000000 4 5 1.337624e-03
## 4282 1.0000000 4 5 1.337624e-03
## 3144 0.9999984 4 10 4.147611e-02
##
## [1] "set_28"
## [1] "RIPOR2" "DUOX1" "MCTP2" "TMEM44"
## [5] "LINC00467" "BEX3" "RAB37" "H2BC4"
## [9] "H2AC20" "MTCP1" "GOLGA8B" "AC023590.1"
## [13] "ZNF451-AS1" "WEE2-AS1" "PCDH9-AS2" "RP11-142A5.1"
## [17] "KCNMA1-AS1" "RP11-544A12.4" "RP5-1101C3.1" "RP11-115J16.1"
## [21] "RP11-120A1.1" "RP11-463D19.1" "RP11-511B23.2" "RP1-71H24.1"
## [25] "TCF4-AS1" "RP11-126O1.4" "TSIX" "H2AC19"
## [29] "RP11-386I14.4" "H2BC8" "H2AC8" "H2BC7"
## [33] "TRG-AS1" "RP11-275G7.2" "GS1-98E2.1" "RP11-21M24.6"
## [37] "RP11-314E10.1" "RP11-399K19.1" "NIBAN2"
## $reactome
## category
## 9 activated pkn1 stimulates transcription of ar androgen receptor regulated genes k
## 76 assembly of the orc complex at the origin of replication
## 89 base excision repair ap site formation
## 247 dna methylation
## 293 ercc6 csb and ehmt2 g9a positively regulate rrna expression
## 453 inhibition of dna recombination at telomere
## 789 recognition and association of dna glycosylase with site containing an affected p
## 863 rho gtpases activate pkns
## 1016 sirt1 negatively regulates rrna expression
## 610 negative epigenetic regulation of rrna expression
## over_represented_pvalue under_represented_pvalue numDEInCat numInCat
## 9 2.398400e-09 1 6 8
## 76 2.398400e-09 1 6 8
## 89 2.398400e-09 1 6 8
## 247 2.398400e-09 1 6 8
## 293 2.398400e-09 1 6 8
## 453 2.398400e-09 1 6 8
## 789 2.398400e-09 1 6 8
## 863 2.398400e-09 1 6 8
## 1016 2.398400e-09 1 6 8
## 610 3.583122e-09 1 6 9
## FDR
## 9 2.427823e-07
## 76 2.427823e-07
## 89 2.427823e-07
## 247 2.427823e-07
## 293 2.427823e-07
## 453 2.427823e-07
## 789 2.427823e-07
## 863 2.427823e-07
## 1016 2.427823e-07
## 610 2.427823e-07
##
## [1] "set_33"
## [1] "OSBPL6" "PDE4D" "RALGPS2" "RFC3" "PIGK" "MAGI1"
## [7] "PTPN14" "SETBP1" "TIAM1" "PLEKHA7" "ATAD5" "DNAH14"
## [13] "WWC3" "PLEKHA5" "PDE4A" "CUX2" "RLF" "ESYT2"
## [19] "DENND1A" "MAPK8IP1" "STARD13" "AGAP3" "DENND4C" "WDR45B"
## [25] "RIT2" "SRSF12" "AGAP1" "FAM110B" "ROBO1" "TANC2"
## [31] "FAM20C" "CADM1" "PDE4B" "SIPA1L1" "RGL3"
## $reactome
## category over_represented_pvalue under_represented_pvalue numDEInCat
## 203 darpp 32 events 2.703721e-05 1 3
## numInCat FDR
## 203 3 0.03195798
##
## [1] "set_38"
## [1] "SNCAIP" "RPH3A" "LRRC74A" "MEIS1" "RORA" "RAB27A" "SMARCD3"
## [8] "CELF4" "TBL1X" "NPDC1" "EPHA4" "AKT3" "EMILIN2" "DRAM1"
## [15] "KCNH1" "PAM" "CLVS2" "LRRC4C" "CLEC1A" "CRIM1" "PDE3B"
## [22] "KALRN" "ZFPM2" "PPM1E" "ALOX15B" "ZDHHC20" "UNC5C" "TSHZ2"
## [29] "EFNA5" "NELL2" "OSBP2" "PBX1" "KAZN" "MIB2" "MICAL3"
## [36] "GRIN2B"
## $reactome
## category over_represented_pvalue
## 899 rora activates gene expression 2.099059e-05
## under_represented_pvalue numDEInCat numInCat FDR
## 899 1 3 3 0.02481088
## used (Mb) gc trigger (Mb) limit (Mb) max used (Mb)
## Ncells 8955030 478.3 16112782 860.6 NA 16112782 860.6
## Vcells 16666630 127.2 31295163 238.8 65536 31295163 238.8
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] goseq_1.50.0 geneLenDataBase_1.34.0 BiasedUrn_2.0.10
## [4] fgsea_1.24.0 biomaRt_2.54.1 limma_3.54.2
## [7] tidyr_1.3.0 ggpubr_0.6.0 ggplot2_3.4.2
## [10] data.table_1.14.8
##
## loaded via a namespace (and not attached):
## [1] nlme_3.1-162 matrixStats_1.0.0
## [3] bitops_1.0-7 bit64_4.0.5
## [5] filelock_1.0.2 progress_1.2.2
## [7] httr_1.4.6 GenomeInfoDb_1.34.9
## [9] tools_4.2.3 backports_1.4.1
## [11] bslib_0.4.2 utf8_1.2.3
## [13] R6_2.5.1 mgcv_1.8-42
## [15] DBI_1.1.3 BiocGenerics_0.44.0
## [17] colorspace_2.1-0 withr_2.5.0
## [19] tidyselect_1.2.0 prettyunits_1.1.1
## [21] bit_4.0.5 curl_5.0.1
## [23] compiler_4.2.3 cli_3.6.1
## [25] Biobase_2.58.0 xml2_1.3.4
## [27] DelayedArray_0.24.0 rtracklayer_1.58.0
## [29] sass_0.4.5 scales_1.2.1
## [31] rappdirs_0.3.3 Rsamtools_2.14.0
## [33] stringr_1.5.0 digest_0.6.31
## [35] rmarkdown_2.21 XVector_0.38.0
## [37] pkgconfig_2.0.3 htmltools_0.5.5
## [39] MatrixGenerics_1.10.0 dbplyr_2.3.2
## [41] fastmap_1.1.1 rlang_1.1.0
## [43] rstudioapi_0.14 RSQLite_2.3.1
## [45] BiocIO_1.8.0 jquerylib_0.1.4
## [47] generics_0.1.3 jsonlite_1.8.4
## [49] BiocParallel_1.32.6 dplyr_1.1.2
## [51] car_3.1-2 RCurl_1.98-1.12
## [53] magrittr_2.0.3 GO.db_3.16.0
## [55] GenomeInfoDbData_1.2.9 Matrix_1.6-4
## [57] Rcpp_1.0.10 munsell_0.5.0
## [59] S4Vectors_0.36.2 fansi_1.0.4
## [61] abind_1.4-5 lifecycle_1.0.3
## [63] stringi_1.7.12 yaml_2.3.7
## [65] carData_3.0-5 SummarizedExperiment_1.28.0
## [67] zlibbioc_1.44.0 org.Hs.eg.db_3.16.0
## [69] BiocFileCache_2.6.1 grid_4.2.3
## [71] blob_1.2.4 parallel_4.2.3
## [73] crayon_1.5.2 lattice_0.20-45
## [75] splines_4.2.3 Biostrings_2.66.0
## [77] cowplot_1.1.1 GenomicFeatures_1.50.4
## [79] hms_1.1.3 KEGGREST_1.38.0
## [81] knitr_1.44 pillar_1.9.0
## [83] GenomicRanges_1.50.2 rjson_0.2.21
## [85] ggsignif_0.6.4 codetools_0.2-19
## [87] stats4_4.2.3 fastmatch_1.1-3
## [89] XML_3.99-0.14 glue_1.6.2
## [91] evaluate_0.20 png_0.1-8
## [93] vctrs_0.6.2 gtable_0.3.3
## [95] purrr_1.0.1 cachem_1.0.7
## [97] xfun_0.39 broom_1.0.4
## [99] restfulr_0.0.15 rstatix_0.7.2
## [101] tibble_3.2.1 GenomicAlignments_1.34.1
## [103] AnnotationDbi_1.60.2 memoise_2.0.1
## [105] IRanges_2.32.0